Examples with VersionFlag org.vcell.util.document.VersionFlag used on opensource projects

Example 1 with VersionFlag

use of org.vcell.util.document.VersionFlag in project vcell by virtualcell.

the class XmlReader method getSimulationVersion.

/**
 * This method returns a Version object from an XML representation.
 * Creation date: (3/16/2001 3:41:24 PM)
 * @return cbit.sql.Version
 * @param param org.jdom.Element
 */
private SimulationVersion getSimulationVersion(Element xmlVersion) throws XmlParseException {
    if (xmlVersion == null) {
        return null;
    }
    // determine if it should be processed using the 'fromVersionable'
    if (xmlVersion.getAttributeValue(XMLTags.FromVersionableTag) == null || Boolean.valueOf(xmlVersion.getAttributeValue(XMLTags.FromVersionableTag)).booleanValue() || this.readKeysFlag == false) {
        // this came from a versionable object, so skip! Or it should not explicitly import the information inside the Version
        return null;
    }
    // Read all the attributes
    // *name
    String name = unMangle(xmlVersion.getAttributeValue(XMLTags.NameAttrTag));
    // *key
    String temp = xmlVersion.getAttributeValue(XMLTags.KeyValueAttrTag);
    KeyValue key = new KeyValue(temp);
    // *owner
    Element tempElement = xmlVersion.getChild(XMLTags.OwnerTag, vcNamespace);
    User owner = new User(unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag)), new KeyValue(tempElement.getAttributeValue(XMLTags.IdentifierAttrTag)));
    // *access
    GroupAccess groupAccess = getGroupAccess(xmlVersion.getChild(XMLTags.GroupAccessTag, vcNamespace));
    // *Branchpointref
    temp = xmlVersion.getAttributeValue(XMLTags.BranchPointRefTag);
    KeyValue branchpointref = null;
    if (temp != null) {
        branchpointref = new KeyValue(temp);
    }
    // *BranchID
    java.math.BigDecimal branchId = new java.math.BigDecimal(xmlVersion.getAttributeValue(XMLTags.BranchIdAttrTag));
    // *Flag
    temp = xmlVersion.getAttributeValue(XMLTags.FlagAttrTag);
    VersionFlag flag = VersionFlag.fromInt(Integer.parseInt(temp));
    // *Date
    java.util.Date date = null;
    temp = xmlVersion.getAttributeValue(XMLTags.DateAttrTag);
    if (temp != null) {
        try {
            SimpleDateFormat simpleDateFormat = new SimpleDateFormat(BeanUtils.vcDateFormat, Locale.US);
            date = simpleDateFormat.parse(temp);
        } catch (java.text.ParseException e) {
            e.printStackTrace();
            throw new XmlParseException("Invalid date:" + temp, e);
        }
    }
    // *DataSimulationRef
    KeyValue parentSimRefKey = null;
    tempElement = xmlVersion.getChild(XMLTags.ParentSimRefTag, vcNamespace);
    if (tempElement != null) {
        parentSimRefKey = new KeyValue(tempElement.getAttributeValue(XMLTags.KeyValueAttrTag));
    }
    // *Annotation
    String annotation = null;
    String annotationText = xmlVersion.getChildText(XMLTags.AnnotationTag, vcNamespace);
    if (annotationText != null && annotationText.length() > 0) {
        annotation = unMangle(annotationText);
    }
    // Create and return the version object
    return new SimulationVersion(key, name, owner, groupAccess, branchpointref, branchId, date, flag, annotation, parentSimRefKey);
}

Example 2 with VersionFlag

use of org.vcell.util.document.VersionFlag in project vcell by virtualcell.

the class XmlReader method getVersion.

/**
 * This method returns a Version object from an XML representation.
 * Creation date: (3/16/2001 3:41:24 PM)
 * @return cbit.sql.Version
 * @param param org.jdom.Element
 */
private Version getVersion(Element xmlVersion) throws XmlParseException {
    if (xmlVersion == null) {
        return null;
    }
    // determine if it should be processed using the 'fromVersionable'
    if (xmlVersion.getAttributeValue(XMLTags.FromVersionableTag) == null || Boolean.valueOf(xmlVersion.getAttributeValue(XMLTags.FromVersionableTag)).booleanValue() || this.readKeysFlag == false) {
        // this came from a versionable object, so skip! Or it should not explicitly import the information inside the Version
        return null;
    }
    // Read all the attributes
    // *name
    String name = unMangle(xmlVersion.getAttributeValue(XMLTags.NameAttrTag));
    // *key
    String temp = xmlVersion.getAttributeValue(XMLTags.KeyValueAttrTag);
    KeyValue key = new KeyValue(temp);
    // *owner
    Element tempElement = xmlVersion.getChild(XMLTags.OwnerTag, vcNamespace);
    User owner = new User(unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag)), new KeyValue(tempElement.getAttributeValue(XMLTags.IdentifierAttrTag)));
    // *access
    GroupAccess groupAccess = getGroupAccess(xmlVersion.getChild(XMLTags.GroupAccessTag, vcNamespace));
    // *Branchpointref
    temp = xmlVersion.getAttributeValue(XMLTags.BranchPointRefTag);
    KeyValue branchpointref = null;
    if (temp != null) {
        branchpointref = new KeyValue(temp);
    }
    // *BranchID
    java.math.BigDecimal branchId = new java.math.BigDecimal(xmlVersion.getAttributeValue(XMLTags.BranchIdAttrTag));
    // *Flag
    temp = xmlVersion.getAttributeValue(XMLTags.FlagAttrTag);
    VersionFlag flag = VersionFlag.fromInt(Integer.parseInt(temp));
    // *Date
    java.util.Date date = null;
    temp = xmlVersion.getAttributeValue(XMLTags.DateAttrTag);
    if (temp != null) {
        try {
            SimpleDateFormat simpleDateFormat = new SimpleDateFormat(BeanUtils.vcDateFormat, Locale.US);
            date = simpleDateFormat.parse(temp);
        } catch (java.text.ParseException e) {
            e.printStackTrace();
            throw new XmlParseException("Invalid date:" + temp, e);
        }
    }
    // *Annotation
    String annotation = null;
    String annotationText = xmlVersion.getChildText(XMLTags.AnnotationTag, vcNamespace);
    if (annotationText != null && annotationText.length() > 0) {
        annotation = unMangle(annotationText);
    }
    // Create and return the version object
    return new Version(key, name, owner, groupAccess, branchpointref, branchId, date, flag, annotation);
}

Example 3 with VersionFlag

use of org.vcell.util.document.VersionFlag in project vcell by virtualcell.

the class DbDriver method curate.

/**
 * Insert the method's description here.
 * Creation date: (5/23/2006 10:44:52 AM)
 */
public static VCDocumentInfo curate(CurateSpec curateSpec, Connection con, User user, DatabaseSyntax dbSyntax) throws DataAccessException, SQLException {
    VersionableType vType = null;
    if (curateSpec.getVCDocumentInfo() instanceof BioModelInfo) {
        vType = VersionableType.BioModelMetaData;
    } else if (curateSpec.getVCDocumentInfo() instanceof MathModelInfo) {
        vType = VersionableType.MathModelMetaData;
    } else {
        throw new DataAccessException("Expecting BioModelInfo or MathModelInfo but got type=" + curateSpec.getVCDocumentInfo().getClass().getName());
    }
    KeyValue vKey = curateSpec.getVCDocumentInfo().getVersion().getVersionKey();
    Version dbVersion = getVersionFromKeyValue(con, vType, vKey);
    // Must be owner to curate
    if (!dbVersion.getOwner().compareEqual(user)) {
        throw new PermissionException("Cannot curate " + vType.getTypeName() + " \"" + dbVersion.getName() + "\" (" + vKey + "), not owned by " + user.getName());
    }
    VersionFlag updatedVersionFlag = null;
    if (curateSpec.getCurateType() == CurateSpec.ARCHIVE) {
        if (!dbVersion.getFlag().compareEqual(VersionFlag.Current)) {
            throw new IllegalArgumentException("Only non-archived, non-published documents can be ARCHIVED");
        }
        updatedVersionFlag = VersionFlag.Archived;
    } else if (curateSpec.getCurateType() == CurateSpec.PUBLISH) {
        // Must have PUBLISH rights
        if (!dbVersion.getOwner().isPublisher()) {
            throw new PermissionException("Cannot curate " + vType.getTypeName() + " \"" + dbVersion.getName() + "\" (" + vKey + "), user " + user.getName() + " not granted PUBLISHING rights");
        }
        // Must be ARCHIVED and Public before PUBLISH is allowed
        if (!dbVersion.getFlag().compareEqual(VersionFlag.Archived) || !(dbVersion.getGroupAccess() instanceof GroupAccessAll)) {
            throw new IllegalArgumentException("Only ARCHIVED documents with PUBLIC permission can be PUBLISHED");
        }
        updatedVersionFlag = VersionFlag.Published;
    } else {
        throw new DataAccessException("Expecting CurateType " + CurateSpec.ARCHIVE + "(ARCHIVE) or " + CurateSpec.PUBLISH + "(PUBLISH) but got type=" + curateSpec.getCurateType());
    }
    VersionTable vTable = VersionTable.getVersionTable(vType);
    String set = vTable.versionFlag.getQualifiedColName() + " = " + updatedVersionFlag.getIntValue();
    String cond = vTable.id.getQualifiedColName() + " = " + vKey;
    String sql = DatabasePolicySQL.enforceOwnershipUpdate(user, vTable, set, cond);
    int numRowsProcessed = updateCleanSQL(con, sql);
    // Clear XML
    if (vType.equals(VersionableType.BioModelMetaData)) {
        updateCleanSQL(con, "DELETE FROM " + BioModelXMLTable.table.getTableName() + " WHERE " + BioModelXMLTable.table.bioModelRef.getQualifiedColName() + " = " + vKey.toString());
    } else if (vType.equals(VersionableType.MathModelMetaData)) {
        updateCleanSQL(con, "DELETE FROM " + MathModelXMLTable.table.getTableName() + " WHERE " + MathModelXMLTable.table.mathModelRef.getQualifiedColName() + " = " + vKey.toString());
    }
    VCDocumentInfo dbVCDocumentInfo = (VCDocumentInfo) getVersionableInfos(con, user, vType, false, vKey, false, dbSyntax).elementAt(0);
    return dbVCDocumentInfo;
}

Example 4 with VersionFlag

use of org.vcell.util.document.VersionFlag in project vcell by virtualcell.

the class DbDriver method insertVersionableInit.

/**
 * This method was created in VisualAge.
 * @return cbit.sql.KeyValue
 * @param versionable cbit.sql.Versionable
 * @param pRef cbit.sql.KeyValue
 * @param bCommit boolean
 */
protected Version insertVersionableInit(InsertHashtable hash, Connection con, User user, Versionable versionable, String name, String annot, boolean bVersion) throws SQLException, DataAccessException {
    if (hash.getDatabaseKey(versionable) != null) {
        throw new DataAccessException(versionable + " already inserted in this transaction");
    }
    VersionableType vType = VersionTable.versionableTypeFromVersionable(versionable);
    if (vType.getIsTopLevel() && isNameUsed(con, vType, user, name)) {
        throw new DataAccessException("'" + user.getName() + "' already has a " + vType.getTypeName() + " with name '" + name + "'");
    }
    User owner = user;
    // AccessInfo accessInfo = new AccessInfo(AccessInfo.PRIVATE_CODE);
    GroupAccess accessInfo = new GroupAccessNone();
    KeyValue versionKey = keyFactory.getNewKey(con);
    java.util.Date date = getNewDate(con);
    // if(versionable.getVersion().getVersionKey() != null){
    // throw new DataAccessException("GeomDbDriver:insertVersionable, VersionKey must be null to insert");
    // }
    String versionName = name;
    // Check for Archive and Publish not needed in insert because versionflag is always forced to Current
    VersionFlag versionFlag = null;
    // if(bVersion){
    // versionFlag = VersionFlag.Archived;
    // }else{
    versionFlag = VersionFlag.Current;
    // }
    KeyValue PRefKey = null;
    java.math.BigDecimal branchID = getNewBranchID(con);
    // 
    // Insert Software Version
    // 
    insertSoftwareVersion(con, versionKey);
    // 
    return new Version(versionKey, versionName, owner, accessInfo, PRefKey, branchID, date, versionFlag, annot);
}

Example 5 with VersionFlag

use of org.vcell.util.document.VersionFlag in project vcell by virtualcell.

the class ClientMDIManager method createCanonicalTitle.

/**
 * Insert the method's description here.
 * Creation date: (5/27/2006 4:10:10 PM)
 * @return java.lang.String
 * @param version cbit.sql.Version
 */
public static String createCanonicalTitle(VCDocument vcDocument) {
    Version version = vcDocument.getVersion();
    VCDocumentType docType = vcDocument.getDocumentType();
    String docName = (version != null ? version.getName() : (vcDocument.getName() == null ? "NoName" : vcDocument.getName() + " (NoVersion)"));
    java.util.Date docDate = (version != null ? version.getDate() : null);
    VersionFlag versionFlag = (version != null ? version.getFlag() : null);
    String title = (versionFlag != null && versionFlag.compareEqual(VersionFlag.Archived) ? "(" + CurateSpec.CURATE_TYPE_STATES[CurateSpec.ARCHIVE] + ") " : "") + (versionFlag != null && versionFlag.compareEqual(VersionFlag.Published) ? "(" + CurateSpec.CURATE_TYPE_STATES[CurateSpec.PUBLISH] + ") " : "") + (docType == VCDocumentType.BIOMODEL_DOC ? "BIOMODEL: " : "") + (docType == VCDocumentType.MATHMODEL_DOC ? "MATHMODEL: " : "") + (docType == VCDocumentType.GEOMETRY_DOC ? "GEOMETRY: " : "") + docName + " " + "(" + (docDate != null ? docDate.toString() : "NoDate") + ")";
    title += " -- VCell " + DocumentWindowAboutBox.getVERSION_NO() + " (build " + DocumentWindowAboutBox.getBUILD_NO() + ")";
    return title;
}